147 research outputs found
Genealogies of rapidly adapting populations
The genetic diversity of a species is shaped by its recent evolutionary
history and can be used to infer demographic events or selective sweeps. Most
inference methods are based on the null hypothesis that natural selection is a
weak or infrequent evolutionary force. However, many species, particularly
pathogens, are under continuous pressure to adapt in response to changing
environments. A statistical framework for inference from diversity data of such
populations is currently lacking. Toward this goal, we explore the properties
of genealogies in a model of continual adaptation in asexual populations. We
show that lineages trace back to a small pool of highly fit ancestors, in which
almost simultaneous coalescence of more than two lineages frequently occurs.
While such multiple mergers are unlikely under the neutral coalescent, they
create a unique genetic footprint in adapting populations. The site frequency
spectrum of derived neutral alleles, for example, is non-monotonic and has a
peak at high frequencies, whereas Tajima's D becomes more and more negative
with increasing sample size. Since multiple merger coalescents emerge in many
models of rapid adaptation, we argue that they should be considered as a
null-model for adapting populations.Comment: to appear in PNA
The rate of beneficial mutations surfing on the wave of a range expansion
Many theoretical and experimental studies suggest that range expansions can
have severe consequences for the gene pool of the expanding population. Due to
strongly enhanced genetic drift at the advancing frontier, neutral and weakly
deleterious mutations can reach large frequencies in the newly colonized
regions, as if they were surfing the front of the range expansion. These
findings raise the question of how frequently beneficial mutations successfully
surf at shifting range margins, thereby promoting adaptation towards a
range-expansion phenotype. Here, we use individual-based simulations to study
the surfing statistics of recurrent beneficial mutations on wave-like range
expansions in linear habitats. We show that the rate of surfing depends on two
strongly antagonistic factors, the probability of surfing given the spatial
location of a novel mutation and the rate of occurrence of mutations at that
location. The surfing probability strongly increases towards the tip of the
wave. Novel mutations are unlikely to surf unless they enjoy a spatial head
start compared to the bulk of the population. The needed head start is shown to
be proportional to the inverse fitness of the mutant type, and only weakly
dependent on the carrying capacity. The second factor is the mutation
occurrence which strongly decreases towards the tip of the wave. Thus, most
successful mutations arise at an intermediate position in the front of the
wave. We present an analytic theory for the tradeoff between these factors that
allows to predict how frequently substitutions by beneficial mutations occur at
invasion fronts. We find that small amounts of genetic drift increase the
fixation rate of beneficial mutations at the advancing front, and thus could be
important for adaptation during species invasions.Comment: 21 pages, 7 figures; to appear in PLoS Computational Biolog
A freely relaxing polymer remembers how it was straightened
The relaxation of initially straight semiflexible polymers has been discussed
mainly with respect to the longest relaxation time. The biologically relevant
non-equilibrium dynamics on shorter times is comparatively poorly understood,
partly because "initially straight" can be realized in manifold ways. Combining
Brownian dynamics simulations and systematic theory, we demonstrate how
different experimental preparations give rise to specific short-time and
universal long-time dynamics. We also discuss boundary effects and the onset of
the stretch--coil transition.Comment: 14 pages, 5 figures, 3 table
Stretching dynamics of semiflexible polymers
We analyze the nonequilibrium dynamics of single inextensible semiflexible biopolymers as stretching forces are applied at the ends. Based on different (contradicting) heuristic arguments, various scaling laws have been proposed for the propagation speed of the backbone tension which is induced in response to stretching. Here, we employ a newly developed unified theory to systematically substantiate, restrict, and extend these approaches. Introducing the practically relevant scenario of a chain equilibrated under some prestretching force f pre that is suddenly exposed to a different external force f ext at the ends, we give a concise physical explanation of the underlying relaxation processes by means of an intuitive blob picture. We discuss the corresponding intermediate asymptotics, derive results for experimentally relevant observables, and support our conclusions by numerical solutions of the coarse-grained equations of motion for the tension
Genetic drift at expanding frontiers promotes gene segregation
Competition between random genetic drift and natural selection plays a
central role in evolution: Whereas non-beneficial mutations often prevail in
small populations by chance, mutations that sweep through large populations
typically confer a selective advantage. Here, however, we observe chance
effects during range expansions that dramatically alter the gene pool even in
large microbial populations. Initially well-mixed populations of two
fluorescently labeled strains of Escherichia coli develop well-defined,
sector-like regions with fractal boundaries in expanding colonies. The
formation of these regions is driven by random fluctuations that originate in a
thin band of pioneers at the expanding frontier. A comparison of bacterial and
yeast colonies (Saccharomyces cerevisiae) suggests that this large-scale
genetic sectoring is a generic phenomenon that may provide a detectable
footprint of past range expansions.Comment: Please visit http://www.pnas.org/content/104/50/19926.abstract for
published articl
Homeostatic competition drives tumor growth and metastasis nucleation
We propose a mechanism for tumor growth emphasizing the role of homeostatic
regulation and tissue stability. We show that competition between surface and
bulk effects leads to the existence of a critical size that must be overcome by
metastases to reach macroscopic sizes. This property can qualitatively explain
the observed size distributions of metastases, while size-independent growth
rates cannot account for clinical and experimental data. In addition, it
potentially explains the observed preferential growth of metastases on tissue
surfaces and membranes such as the pleural and peritoneal layers, suggests a
mechanism underlying the seed and soil hypothesis introduced by Stephen Paget
in 1889 and yields realistic values for metastatic inefficiency. We propose a
number of key experiments to test these concepts. The homeostatic pressure as
introduced in this work could constitute a quantitative, experimentally
accessible measure for the metastatic potential of early malignant growths.Comment: 13 pages, 11 figures, to be published in the HFSP Journa
Population dynamics in compressible flows
Organisms often grow, migrate and compete in liquid environments, as well as
on solid surfaces. However, relatively little is known about what happens when
competing species are mixed and compressed by fluid turbulence. In these
lectures we review our recent work on population dynamics and population
genetics in compressible velocity fields of one and two dimensions. We discuss
why compressible turbulence is relevant for population dynamics in the ocean
and we consider cases both where the velocity field is turbulent and when it is
static. Furthermore, we investigate populations in terms of a continuos density
field and when the populations are treated via discrete particles. In the last
case we focus on the competition and fixation of one species compared to
anotherComment: 16 pages, talk delivered at the Geilo Winter School 201
Mechanically driven growth of quasi-two dimensional microbial colonies
We study colonies of non-motile, rod-shaped bacteria growing on solid
substrates. In our model, bacteria interact purely mechanically, by pushing
each other away as they grow, and consume a diffusing nutrient. We show that
mechanical interactions control the velocity and shape of the advancing front,
which leads to features that cannot be captured by established
Fisher-Kolmogorov models. In particular, we find that the velocity depends on
the elastic modulus of bacteria or their stickiness to the surface.
Interestingly, we predict that the radius of an incompressible, strictly
two-dimensional colony cannot grow linearly in time. Importantly, mechanical
interactions can also account for the nonequilibrium transition between
circular and branching colonies, often observed in the lab.Comment: 5 pages, 4 colour figure
Dynamic structure factor of a stiff polymer in a glassy solution
We provide a comprehensive overview of the current theoretical understanding
of the dynamic structure factor of stiff polymers in semidilute solution based
on the wormlike chain (WLC) model. We extend previous work by computing exact
numerical coefficients and an expression for the dynamic mean square
displacement (MSD) of a free polymer and compare various common approximations
for the hydrodynamic interactions, which need to be treated accurately if one
wants to extract quantitative estimates for model parameters from experimental
data. A recent controversy about the initial slope of the dynamic structure
factor is thereby resolved. To account for the interactions of the polymer with
a surrounding (sticky) polymer solution, we analyze an extension of the WLC
model, the glassy wormlike chain (GWLC), which predicts near power-law and
logarithmic long-time tails in the dynamic structure factor.Comment: 14 pages, 5 figures, final versio
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